With apt-get and yum you're installing pre-built binaries. This works well if that's all you need to do and are okay with the versions that are installed (typically not the latest unless it's a new distribution).

Once you start having to download and build source for apps/libraries that aren't pre-packaged you can run into issues about version compatibilities, where files are located, do you need to download additional packages (*-dev), etc. Having a service that takes care of this for you solves a lot of headaches (part of why rayburst got built in the first place).

Then it sounds like gentoo emerge for other distro. It is useful for setup the software stack base, but I still have to log into the server to configure the software and deploy my code.

In my opinion, you either use PaaS or use chef/puppet, depending on your case.

The issue is that unless you have standards such as directory locations and structure, users and permissions, there isn't a way to automate the process of code deployment even with chef/puppet.

PaaS works because the provider has a standard and forces you to follow them. I don't mean that in any negative sense. I was in SCM for a number of years and know that kind of enforcement is necessary if you want to have any kind of repeatable, automatable and supportable deployments.